BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237588.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,280,309 number of mapped reads = 1,029,487 (80.41%) number of supplementary alignments = 5,518 (0.43%) number of secondary alignments = 0 number of mapped bases = 64,643,146 bp number of sequenced bases = 64,604,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,101 duplication rate = 3.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.0628 >>>>>>> ACTG content number of A's = 16,702,901 bp (25.85%) number of C's = 11,643,156 bp (18.02%) number of T's = 19,784,842 bp (30.62%) number of G's = 16,431,671 bp (25.43%) number of N's = 41,536 bp (0.06%) GC percentage = 43.46% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 644,616 number of insertions = 6,264 mapped reads with insertion percentage = 0.6% number of deletions = 23,693 mapped reads with deletion percentage = 2.27% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 0.0209X std coverageData = 0.2292X There is a 1.72% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 5548460 0.022260566403964947 0.27404727377776816 chr2 243199373 5732475 0.023571092841592152 0.3314428159915564 chr3 198022430 4555218 0.023003545608444458 0.19019673293789907 chr4 191154276 4076785 0.021327197514535327 0.19125692168618566 chr5 180915260 3612603 0.019968481376308442 0.1712989005040263 chr6 171115067 3398560 0.01986125511671044 0.18805546674596618 chr7 159138663 3823635 0.02402706500053981 0.3179136387895874 chr8 146364022 3407391 0.023280249841726816 0.2237565001288049 chr9 141213431 2618045 0.01853963168701708 0.24588108204027587 chr10 135534747 2788492 0.02057400085012886 0.21858778257845546 chr11 135006516 2691875 0.019938852432870722 0.23612163067359554 chr12 133851895 3775632 0.028207534902662378 0.21957623291458647 chr13 115169878 2184749 0.018969795209820402 0.17315238436251554 chr14 107349540 1795534 0.0167260521097715 0.17623967501638343 chr15 102531392 2020333 0.019704531076687227 0.18078414587398486 chr16 90354753 1751968 0.01938988201317976 0.1912658832659897 chr17 81195210 1571970 0.019360378524792287 0.18204434806763098 chr18 78077248 1658355 0.021239926386749697 0.3391367517197941 chr19 59128983 1248298 0.02111144039125449 0.223070486299592 chr20 63025520 1293976 0.020530984908970207 0.18270021609615758 chr21 48129895 781198 0.016231034786176036 0.16868891759536592 chr22 51304566 703986 0.013721702664827142 0.14678796951917233 chrMT 16571 50776 3.064148210729588 2.7114879891719625 chrX 155270560 3317526 0.021366097990501227 0.19192233771952374 chrY 59373566 235306 0.003963144137241142 0.10463947964033696